One of the deaths was that of a 72-year-old woman who was unable to leave her car when it became trapped as a river broke its banks near the village of Solre-Saint-Géry close to the French border.
News reports said the bodies of two other flood victims were found by emergency services in the same area.
Further east in the region of Brabant the general hospital of Tubize was closed and it patients were evacuated.
Flanders was less severely affected, but provincial disaster plans were still activated. Prime Minister Yves Leterme decided not to deploy national disaster measures saying the national situation was under control, although these were the worst floods in 50 years and affected services on both the Thalys and Eurostar rail services.
